calcHpSim {PCAN} | R Documentation

## Compare HP terms based on semantic similarity

### Description

This function compares 2 HP terms based on provided Information Content and ancestors

### Usage

    calcHpSim(term1, term2, method = c("Resnik"), IC, ancestors)

### Arguments

`term1` | one of the HP term to compare
`term2` | the other HP term to compare
`method` | the method for computing semantic simalirity (default: "Resnik" returns the IC of the MICA: Most Informative common ancestor)
`IC` | a named vector of Information Content by HP term
`ancestors` | a named list of ancestors by HP term

### Value

A numeric value

### Author(s)

Patrice Godard

### See Also

`compareHPSets`

### Examples

    ## Prerequisite
    data(geneByHp, hp_descendants, package="PCAN")
    geneByHp <- unstack(geneByHp, entrez~hp)
    ic <- computeHpIC(geneByHp, hp_descendants)

    ## Compute similarity between different couples of HP terms
    data(hp_ancestors, hpDef, package="PCAN")
    hp1 <- "HP:0000518"
    hp2 <- "HP:0030084"
    hp3 <- "HP:0002119"
    hp4 <- "HP:0001305"
    hpDef[which(hpDef$id %in% c(hp1, hp2)), 1:2]
    calcHpSim(hp1, hp2, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp2, hp3)), 1:2]
    calcHpSim(hp2, hp3, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp2, hp4)), 1:2]
    calcHpSim(hp2, hp4, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp3, hp4)), 1:2]
    calcHpSim(hp3, hp4, IC=ic, ancestors=hp_ancestors)

[Package PCAN version 1.22.0 Index]